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Draw the molecule correctly please

Now I have just finished the first undergrad teaching event of the year, I saw a few molecules which were not quite correctly drawn. The problem is that as we learn if we draw things in a way that they can not exist in real life we can sometimes miss out on some important details.

Rather than the details being the bane of our lives we should regard the little details as useful clues which have been placed in the molecules which we will study and use in the first year class. By drawing them as correctly as possible we can remind ourselves of the key points rather than losing the important points like the baby who goes down the plug hole along with the bath water.

Rather than naming and shaming a student for a minor error of molecule drawing which is likely to have been committed unknowingly as a result of inexperience, I thought that as the chemistry teacher I should draw four objects as badly as I can as part of a teaching event for you all.

Good and bad ways to draw four things.

On the left is the worst drawing I was able to think of while on the right is a far better drawing. Now we will go through these objects and try to learn from them. The first one is imadazole, a five memebered ring compound which we will meet again after christmas. On the left it is important to note that the lone pair appears to be inside the five membered ring and is pointing towards the centre of the ring. In real life the lone pair (seen as :  ) is on the outside of the ring point out into space. I have left out the other electron pair which is on nitrogen, this is because it is so hard to draw and because if would distract from the matter at hand.

The next item is a cat, the picture on the left is either a very exotic cat or a rather deformed cat’s head where the ears are on the lower jaw of the cat. The problem with this cat is when it attempts to eat or drink that its ears fill up with either cat food or water (note cats should not be given cow’s milk, it is bad for them). The cat on the right has the ears in the right place and it is likely to have a much better life.
The next item is a heterocycle which is a bit like a uracil, Oh it looks just like the double enol form of uracil. But it has a grave set of errors, on the left the lone pairs are inside the ring and one of the hydroxyl groups is also inside the ring. I think that for a six membered ring that this hydroxyl inside the ring is impossible. The hydroxyl oxygen will stick out away from the centre of the ring and not towards it.
The last thing is the acetylene cis-trans-diene ester, on the left side the acetylene which has sp carbon centres is very unlinear while one of the double bonds is linear. Also the carbonyl oxygen and the methoxy group of the ester are bent away from their ideal locations. These errors which I have paraded before you today might seem trivial but they might be a problem for the developing organic chemistry student. Those of us who have done organic chemistry before will be able to look at the badly drawn molecules and see through the bad drawing to be able to visualise the molecules correctly in our heads but the less experienced chemistry student might be fooled by some of these dire drawings on the left.
The following rules have help you stay and get out of trouble.
1. A sp3 centre is normally tetrahedral, if you include the lone pairs you may get distorted tetrahedra but a trigonal based pyramid is still at heart a tetrahedron.
2. A sp2 centre is normally a trigonal planar thing, examples appear in benzene and ethylene, a harder one is for the nitrogens and oxygens which are sp2. The lack of a atom might fool you, so be careful of these. I can think of molecules where the oxygen is sp2 and some (like water) where it is sp3.
3. A sp centre is linear, think of dinitrogen (nitrogen gas), acetylene (C2H2), carbon monoxide and hydrogen cyanide. Be careful that many molecules have atoms with different hybridization in them. For example carbon dioxide has a sp carbon and two sp2 oxygens while allene has a sp carbon in the middle and two sp2 carbons on the ends.
4. When doing organic chemistry, I would advise when you are stuck to use VSEPR. While VSEPR does not work well for transition metal compounds like cisplatin it does work for many main group compounds. It gets the answer right most of the time as long as you do not have a stereochemically inactive lone pair as is found sometimes on lead, tellurium and some other heavy atoms.

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